Starting phenix.real_space_refine on Fri Oct 10 19:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwn_35774/10_2025/8iwn_35774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwn_35774/10_2025/8iwn_35774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwn_35774/10_2025/8iwn_35774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwn_35774/10_2025/8iwn_35774.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwn_35774/10_2025/8iwn_35774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwn_35774/10_2025/8iwn_35774.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.147 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5682 2.51 5 N 1470 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8764 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4350 Classifications: {'peptide': 559} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 540} Chain breaks: 4 Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4350 Classifications: {'peptide': 559} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 540} Chain breaks: 4 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.31, per 1000 atoms: 0.26 Number of scatterers: 8764 At special positions: 0 Unit cell: (100.1, 75.9, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 O 1546 8.00 N 1470 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 622 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 343.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 58.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.733A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.507A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.579A pdb=" N GLU A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.777A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.521A pdb=" N GLY A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.753A pdb=" N PHE A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.964A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.731A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.541A pdb=" N THR A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.641A pdb=" N LEU A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.888A pdb=" N LYS A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.505A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.915A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.697A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.545A pdb=" N GLY A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.505A pdb=" N MET A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 507 removed outlier: 3.551A pdb=" N VAL A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix removed outlier: 3.611A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.577A pdb=" N THR A 519 " --> pdb=" O PRO A 515 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 removed outlier: 4.223A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.736A pdb=" N MET A 576 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.230A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 623 through 627 removed outlier: 3.590A pdb=" N GLU A 627 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.635A pdb=" N LEU A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.524A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.732A pdb=" N LEU C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 169 removed outlier: 3.506A pdb=" N PHE C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.580A pdb=" N GLU C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.778A pdb=" N ARG C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 256 removed outlier: 3.521A pdb=" N GLY C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.754A pdb=" N PHE C 275 " --> pdb=" O PHE C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.965A pdb=" N SER C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.731A pdb=" N LEU C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.541A pdb=" N THR C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 349 removed outlier: 3.642A pdb=" N LEU C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.887A pdb=" N LYS C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 408 through 425 removed outlier: 3.505A pdb=" N VAL C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 455 removed outlier: 3.916A pdb=" N GLY C 438 " --> pdb=" O HIS C 434 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Proline residue: C 451 - end of helix removed outlier: 3.697A pdb=" N ASN C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 473 removed outlier: 3.545A pdb=" N GLY C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.506A pdb=" N MET C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS C 484 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 488 " --> pdb=" O HIS C 484 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 489 " --> pdb=" O VAL C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 507 removed outlier: 3.551A pdb=" N VAL C 494 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix removed outlier: 3.611A pdb=" N THR C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 541 removed outlier: 3.577A pdb=" N THR C 519 " --> pdb=" O PRO C 515 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 561 removed outlier: 4.223A pdb=" N THR C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.736A pdb=" N MET C 576 " --> pdb=" O MET C 573 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 577 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 removed outlier: 4.230A pdb=" N TYR C 584 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 588 " --> pdb=" O TYR C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 604 Processing helix chain 'C' and resid 623 through 627 removed outlier: 3.592A pdb=" N GLU C 627 " --> pdb=" O PHE C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.635A pdb=" N LEU C 642 " --> pdb=" O SER C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 658 removed outlier: 3.524A pdb=" N TYR C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 653 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 6.452A pdb=" N TYR A 47 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 85 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 45 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 87 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 43 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY A 89 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A 41 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE A 42 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU A 128 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.341A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASP A 231 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL A 145 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 277 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 81 through 91 removed outlier: 6.451A pdb=" N TYR C 47 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 85 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 45 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 87 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL C 43 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY C 89 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS C 41 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE C 42 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU C 128 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP C 44 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS C 126 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 142 through 145 removed outlier: 6.341A pdb=" N GLY C 143 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP C 231 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL C 145 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 277 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 278 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 289 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 280 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2613 1.33 - 1.45: 1520 1.45 - 1.57: 4709 1.57 - 1.69: 10 1.69 - 1.81: 92 Bond restraints: 8944 Sorted by residual: bond pdb=" C4 ATP C 701 " pdb=" C5 ATP C 701 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.29e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.26e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.47e+01 bond pdb=" C5 ATP C 701 " pdb=" C6 ATP C 701 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.39e+01 bond pdb=" C4 ATP C 701 " pdb=" N9 ATP C 701 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.55e+01 ... (remaining 8939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 11641 2.73 - 5.46: 413 5.46 - 8.19: 56 8.19 - 10.93: 18 10.93 - 13.66: 6 Bond angle restraints: 12134 Sorted by residual: angle pdb=" PB ATP C 701 " pdb=" O3B ATP C 701 " pdb=" PG ATP C 701 " ideal model delta sigma weight residual 139.87 126.21 13.66 1.00e+00 1.00e+00 1.87e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 126.25 13.62 1.00e+00 1.00e+00 1.85e+02 angle pdb=" PA ATP C 701 " pdb=" O3A ATP C 701 " pdb=" PB ATP C 701 " ideal model delta sigma weight residual 136.83 128.20 8.63 1.00e+00 1.00e+00 7.45e+01 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 128.22 8.61 1.00e+00 1.00e+00 7.41e+01 angle pdb=" C5 ATP C 701 " pdb=" C4 ATP C 701 " pdb=" N3 ATP C 701 " ideal model delta sigma weight residual 126.80 119.11 7.69 1.00e+00 1.00e+00 5.92e+01 ... (remaining 12129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 4981 15.76 - 31.52: 255 31.52 - 47.28: 56 47.28 - 63.04: 4 63.04 - 78.80: 8 Dihedral angle restraints: 5304 sinusoidal: 2104 harmonic: 3200 Sorted by residual: dihedral pdb=" CA SER A 405 " pdb=" C SER A 405 " pdb=" N PHE A 406 " pdb=" CA PHE A 406 " ideal model delta harmonic sigma weight residual 180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA SER C 405 " pdb=" C SER C 405 " pdb=" N PHE C 406 " pdb=" CA PHE C 406 " ideal model delta harmonic sigma weight residual -180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ASP C 176 " pdb=" C ASP C 176 " pdb=" N VAL C 177 " pdb=" CA VAL C 177 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 952 0.063 - 0.127: 414 0.127 - 0.190: 55 0.190 - 0.253: 15 0.253 - 0.316: 6 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CB VAL C 456 " pdb=" CA VAL C 456 " pdb=" CG1 VAL C 456 " pdb=" CG2 VAL C 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB VAL A 456 " pdb=" CA VAL A 456 " pdb=" CG1 VAL A 456 " pdb=" CG2 VAL A 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB ILE A 91 " pdb=" CA ILE A 91 " pdb=" CG1 ILE A 91 " pdb=" CG2 ILE A 91 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1439 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 96 " 0.019 2.00e-02 2.50e+03 1.98e-02 6.83e+00 pdb=" CG PHE C 96 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 96 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 96 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 96 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 96 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 96 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 96 " -0.019 2.00e-02 2.50e+03 1.96e-02 6.74e+00 pdb=" CG PHE A 96 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 96 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 96 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 96 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 96 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 96 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 569 " 0.043 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 570 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 570 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 570 " 0.035 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3190 2.90 - 3.40: 7618 3.40 - 3.90: 13108 3.90 - 4.40: 16119 4.40 - 4.90: 27439 Nonbonded interactions: 67474 Sorted by model distance: nonbonded pdb=" N ASP C 238 " pdb=" OD1 ASP C 238 " model vdw 2.398 3.120 nonbonded pdb=" N ASP A 238 " pdb=" OD1 ASP A 238 " model vdw 2.398 3.120 nonbonded pdb=" O ASN C 336 " pdb=" OG1 THR C 340 " model vdw 2.401 3.040 nonbonded pdb=" O ASN A 336 " pdb=" OG1 THR A 340 " model vdw 2.401 3.040 nonbonded pdb=" O THR C 192 " pdb=" OG1 THR C 192 " model vdw 2.419 3.040 ... (remaining 67469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 701) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.250 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.114 8946 Z= 0.566 Angle : 1.217 13.657 12138 Z= 0.681 Chirality : 0.069 0.316 1442 Planarity : 0.008 0.064 1478 Dihedral : 10.546 78.801 3242 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.96 (0.17), residues: 1098 helix: -4.65 (0.08), residues: 626 sheet: -0.59 (0.56), residues: 82 loop : -3.07 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 587 TYR 0.023 0.003 TYR C 526 PHE 0.045 0.004 PHE C 96 TRP 0.030 0.005 TRP A 426 HIS 0.016 0.004 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.01322 ( 8944) covalent geometry : angle 1.21671 (12134) SS BOND : bond 0.00130 ( 2) SS BOND : angle 1.17167 ( 4) hydrogen bonds : bond 0.35167 ( 358) hydrogen bonds : angle 9.75187 ( 1044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.370 Fit side-chains REVERT: A 50 LYS cc_start: 0.8042 (ttmp) cc_final: 0.7808 (tttp) REVERT: A 491 MET cc_start: 0.7966 (tpp) cc_final: 0.7619 (tpt) REVERT: A 545 LYS cc_start: 0.9252 (tttm) cc_final: 0.9044 (tttt) REVERT: A 599 GLU cc_start: 0.7530 (tt0) cc_final: 0.6110 (pm20) REVERT: C 50 LYS cc_start: 0.7998 (ttmp) cc_final: 0.7751 (tttp) REVERT: C 202 THR cc_start: 0.8611 (p) cc_final: 0.8356 (t) REVERT: C 491 MET cc_start: 0.7983 (tpp) cc_final: 0.7639 (tpt) REVERT: C 545 LYS cc_start: 0.9243 (tttm) cc_final: 0.9040 (tttt) REVERT: C 599 GLU cc_start: 0.7559 (tt0) cc_final: 0.6193 (pm20) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.9154 time to fit residues: 113.6878 Evaluate side-chains 84 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS C 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.136603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.105571 restraints weight = 9842.243| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.63 r_work: 0.2942 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8946 Z= 0.117 Angle : 0.570 6.479 12138 Z= 0.301 Chirality : 0.042 0.154 1442 Planarity : 0.006 0.063 1478 Dihedral : 7.663 65.437 1278 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.37 % Allowed : 6.42 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.21), residues: 1098 helix: -2.78 (0.15), residues: 650 sheet: -0.73 (0.49), residues: 110 loop : -2.36 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.013 0.001 TYR A 586 PHE 0.016 0.001 PHE A 96 TRP 0.014 0.001 TRP C 447 HIS 0.007 0.001 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8944) covalent geometry : angle 0.57011 (12134) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.62579 ( 4) hydrogen bonds : bond 0.04863 ( 358) hydrogen bonds : angle 4.48576 ( 1044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 277 THR cc_start: 0.8984 (m) cc_final: 0.8649 (p) REVERT: A 403 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.6265 (p90) REVERT: A 489 LEU cc_start: 0.8127 (tt) cc_final: 0.7626 (mp) REVERT: A 491 MET cc_start: 0.8452 (tpp) cc_final: 0.8093 (tpt) REVERT: A 599 GLU cc_start: 0.7433 (tt0) cc_final: 0.5789 (pm20) REVERT: C 202 THR cc_start: 0.8448 (p) cc_final: 0.8150 (t) REVERT: C 277 THR cc_start: 0.8989 (m) cc_final: 0.8672 (p) REVERT: C 403 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.6276 (p90) REVERT: C 491 MET cc_start: 0.8401 (tpp) cc_final: 0.8032 (tpt) REVERT: C 599 GLU cc_start: 0.7475 (tt0) cc_final: 0.5859 (pm20) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.7762 time to fit residues: 89.0622 Evaluate side-chains 97 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.130306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099364 restraints weight = 9803.998| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.59 r_work: 0.2847 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8946 Z= 0.234 Angle : 0.674 7.692 12138 Z= 0.345 Chirality : 0.049 0.174 1442 Planarity : 0.006 0.074 1478 Dihedral : 7.868 59.999 1278 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.21 % Allowed : 8.84 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.23), residues: 1098 helix: -1.80 (0.18), residues: 654 sheet: 0.09 (0.57), residues: 82 loop : -2.21 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.019 0.002 TYR C 526 PHE 0.021 0.002 PHE C 96 TRP 0.012 0.002 TRP C 447 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 8944) covalent geometry : angle 0.67376 (12134) SS BOND : bond 0.00126 ( 2) SS BOND : angle 1.03637 ( 4) hydrogen bonds : bond 0.06545 ( 358) hydrogen bonds : angle 4.32720 ( 1044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.355 Fit side-chains REVERT: A 403 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.6646 (p90) REVERT: A 491 MET cc_start: 0.8413 (tpp) cc_final: 0.8100 (tpt) REVERT: A 599 GLU cc_start: 0.7571 (tt0) cc_final: 0.5754 (pm20) REVERT: C 202 THR cc_start: 0.8576 (p) cc_final: 0.8366 (t) REVERT: C 403 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.6684 (p90) REVERT: C 431 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7781 (mtt180) REVERT: C 491 MET cc_start: 0.8403 (tpp) cc_final: 0.8094 (tpt) REVERT: C 599 GLU cc_start: 0.7572 (tt0) cc_final: 0.5734 (pm20) outliers start: 21 outliers final: 13 residues processed: 100 average time/residue: 0.7346 time to fit residues: 77.5930 Evaluate side-chains 96 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 31 optimal weight: 0.0030 chunk 32 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS C 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.128937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.097476 restraints weight = 9869.428| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.65 r_work: 0.2827 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8946 Z= 0.234 Angle : 0.662 7.798 12138 Z= 0.339 Chirality : 0.049 0.180 1442 Planarity : 0.005 0.075 1478 Dihedral : 7.897 61.676 1278 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.95 % Allowed : 9.37 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.24), residues: 1098 helix: -1.45 (0.19), residues: 656 sheet: 0.23 (0.56), residues: 82 loop : -2.05 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 396 TYR 0.016 0.002 TYR A 526 PHE 0.018 0.002 PHE C 96 TRP 0.012 0.002 TRP A 447 HIS 0.009 0.001 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 8944) covalent geometry : angle 0.66149 (12134) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.96506 ( 4) hydrogen bonds : bond 0.06210 ( 358) hydrogen bonds : angle 4.22911 ( 1044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.334 Fit side-chains REVERT: A 136 LYS cc_start: 0.8933 (tptm) cc_final: 0.8561 (tptp) REVERT: A 403 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.7304 (p90) REVERT: A 491 MET cc_start: 0.8485 (tpp) cc_final: 0.8212 (tpt) REVERT: A 599 GLU cc_start: 0.7659 (tt0) cc_final: 0.5886 (pm20) REVERT: C 202 THR cc_start: 0.8628 (p) cc_final: 0.8421 (t) REVERT: C 431 ARG cc_start: 0.8229 (mtt90) cc_final: 0.8006 (mtt180) REVERT: C 491 MET cc_start: 0.8485 (tpp) cc_final: 0.8197 (tpt) REVERT: C 599 GLU cc_start: 0.7647 (tt0) cc_final: 0.5881 (pm20) outliers start: 28 outliers final: 19 residues processed: 104 average time/residue: 0.6828 time to fit residues: 75.2320 Evaluate side-chains 101 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.133984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.102572 restraints weight = 9791.668| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.64 r_work: 0.2897 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8946 Z= 0.109 Angle : 0.519 5.245 12138 Z= 0.273 Chirality : 0.042 0.153 1442 Planarity : 0.004 0.075 1478 Dihedral : 7.091 63.248 1278 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.32 % Allowed : 10.63 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.25), residues: 1098 helix: -0.93 (0.20), residues: 650 sheet: -0.24 (0.47), residues: 110 loop : -1.88 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.010 0.001 TYR C 526 PHE 0.010 0.001 PHE C 499 TRP 0.010 0.001 TRP C 447 HIS 0.007 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8944) covalent geometry : angle 0.51935 (12134) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.63026 ( 4) hydrogen bonds : bond 0.04109 ( 358) hydrogen bonds : angle 3.93091 ( 1044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.336 Fit side-chains REVERT: A 136 LYS cc_start: 0.8830 (tptm) cc_final: 0.8453 (tptp) REVERT: A 402 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7295 (ttt-90) REVERT: A 403 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6415 (p90) REVERT: A 491 MET cc_start: 0.8402 (tpp) cc_final: 0.8075 (tpt) REVERT: A 599 GLU cc_start: 0.7536 (tt0) cc_final: 0.5701 (pm20) REVERT: A 626 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7556 (pm20) REVERT: C 136 LYS cc_start: 0.8878 (tptm) cc_final: 0.8513 (tptp) REVERT: C 402 ARG cc_start: 0.7660 (mtt-85) cc_final: 0.7331 (tpp80) REVERT: C 403 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6545 (p90) REVERT: C 491 MET cc_start: 0.8433 (tpp) cc_final: 0.8094 (tpt) REVERT: C 599 GLU cc_start: 0.7530 (tt0) cc_final: 0.5701 (pm20) outliers start: 22 outliers final: 10 residues processed: 100 average time/residue: 0.7198 time to fit residues: 76.0713 Evaluate side-chains 95 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS C 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.131646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.099723 restraints weight = 9730.162| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.68 r_work: 0.2863 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8946 Z= 0.150 Angle : 0.557 5.994 12138 Z= 0.289 Chirality : 0.044 0.154 1442 Planarity : 0.005 0.074 1478 Dihedral : 7.201 61.594 1278 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.74 % Allowed : 10.21 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.25), residues: 1098 helix: -0.77 (0.20), residues: 654 sheet: -0.12 (0.47), residues: 110 loop : -1.81 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 431 TYR 0.012 0.001 TYR C 586 PHE 0.013 0.001 PHE A 499 TRP 0.011 0.002 TRP A 447 HIS 0.007 0.001 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8944) covalent geometry : angle 0.55683 (12134) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.72953 ( 4) hydrogen bonds : bond 0.04872 ( 358) hydrogen bonds : angle 3.95039 ( 1044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8849 (tptm) cc_final: 0.8542 (tptp) REVERT: A 402 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7331 (ttt-90) REVERT: A 403 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7279 (p90) REVERT: A 491 MET cc_start: 0.8384 (tpp) cc_final: 0.8067 (tpt) REVERT: A 599 GLU cc_start: 0.7561 (tt0) cc_final: 0.5765 (pm20) REVERT: A 626 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7542 (pm20) REVERT: A 627 GLU cc_start: 0.8214 (mp0) cc_final: 0.7328 (mp0) REVERT: A 650 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.5985 (mtt90) REVERT: C 136 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8545 (tptp) REVERT: C 402 ARG cc_start: 0.7641 (mtt-85) cc_final: 0.7344 (tpp80) REVERT: C 403 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.7305 (p90) REVERT: C 489 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7784 (mp) REVERT: C 491 MET cc_start: 0.8461 (tpp) cc_final: 0.8121 (tpt) REVERT: C 599 GLU cc_start: 0.7546 (tt0) cc_final: 0.5762 (pm20) REVERT: C 627 GLU cc_start: 0.8264 (mp0) cc_final: 0.7626 (mp0) REVERT: C 650 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.5983 (mtt90) outliers start: 26 outliers final: 13 residues processed: 103 average time/residue: 0.7059 time to fit residues: 76.9477 Evaluate side-chains 105 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS C 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097961 restraints weight = 9804.742| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.68 r_work: 0.2841 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8946 Z= 0.201 Angle : 0.614 8.776 12138 Z= 0.314 Chirality : 0.047 0.170 1442 Planarity : 0.005 0.075 1478 Dihedral : 7.432 59.430 1278 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.26 % Allowed : 10.11 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.25), residues: 1098 helix: -0.78 (0.20), residues: 656 sheet: 0.60 (0.57), residues: 82 loop : -1.77 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 396 TYR 0.012 0.002 TYR A 586 PHE 0.014 0.002 PHE C 96 TRP 0.011 0.002 TRP C 447 HIS 0.009 0.002 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 8944) covalent geometry : angle 0.61432 (12134) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.87102 ( 4) hydrogen bonds : bond 0.05557 ( 358) hydrogen bonds : angle 4.04479 ( 1044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.357 Fit side-chains REVERT: A 136 LYS cc_start: 0.8892 (tptm) cc_final: 0.8596 (tptp) REVERT: A 403 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.7276 (p90) REVERT: A 491 MET cc_start: 0.8372 (tpp) cc_final: 0.8050 (tpt) REVERT: A 599 GLU cc_start: 0.7613 (tt0) cc_final: 0.5802 (pm20) REVERT: A 627 GLU cc_start: 0.8252 (mp0) cc_final: 0.7613 (mp0) REVERT: A 650 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.6118 (mtt90) REVERT: C 136 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8567 (tptp) REVERT: C 402 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7102 (ttt-90) REVERT: C 403 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7197 (p90) REVERT: C 491 MET cc_start: 0.8483 (tpp) cc_final: 0.8157 (tpt) REVERT: C 599 GLU cc_start: 0.7663 (tt0) cc_final: 0.5886 (pm20) REVERT: C 626 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7502 (pm20) REVERT: C 627 GLU cc_start: 0.8250 (mp0) cc_final: 0.7367 (mp0) REVERT: C 650 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.6118 (mtt90) outliers start: 31 outliers final: 21 residues processed: 106 average time/residue: 0.7139 time to fit residues: 80.0290 Evaluate side-chains 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ARG Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.133794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.101915 restraints weight = 9645.776| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.67 r_work: 0.2896 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8946 Z= 0.102 Angle : 0.509 7.488 12138 Z= 0.264 Chirality : 0.042 0.152 1442 Planarity : 0.004 0.075 1478 Dihedral : 6.903 64.043 1278 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.63 % Allowed : 10.95 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.26), residues: 1098 helix: -0.30 (0.21), residues: 650 sheet: 0.10 (0.47), residues: 110 loop : -1.61 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 431 TYR 0.009 0.001 TYR C 586 PHE 0.010 0.001 PHE A 499 TRP 0.009 0.001 TRP A 447 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8944) covalent geometry : angle 0.50854 (12134) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.56169 ( 4) hydrogen bonds : bond 0.03782 ( 358) hydrogen bonds : angle 3.83256 ( 1044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.350 Fit side-chains REVERT: A 136 LYS cc_start: 0.8803 (tptm) cc_final: 0.8494 (tptp) REVERT: A 491 MET cc_start: 0.8328 (tpp) cc_final: 0.8016 (tpt) REVERT: A 599 GLU cc_start: 0.7509 (tt0) cc_final: 0.5694 (pm20) REVERT: A 626 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7464 (pm20) REVERT: A 627 GLU cc_start: 0.8197 (mp0) cc_final: 0.7272 (mp0) REVERT: A 650 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.5985 (mtt90) REVERT: C 136 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8432 (tptp) REVERT: C 489 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7792 (mp) REVERT: C 491 MET cc_start: 0.8440 (tpp) cc_final: 0.8115 (tpt) REVERT: C 492 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: C 599 GLU cc_start: 0.7502 (tt0) cc_final: 0.5696 (pm20) REVERT: C 626 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7500 (pm20) REVERT: C 627 GLU cc_start: 0.8290 (mp0) cc_final: 0.7386 (mp0) REVERT: C 650 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.5989 (mtt90) outliers start: 25 outliers final: 14 residues processed: 104 average time/residue: 0.7066 time to fit residues: 77.7001 Evaluate side-chains 108 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.0020 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS C 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.130470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098913 restraints weight = 9683.133| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.65 r_work: 0.2827 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8946 Z= 0.205 Angle : 0.619 8.796 12138 Z= 0.315 Chirality : 0.048 0.172 1442 Planarity : 0.005 0.075 1478 Dihedral : 7.394 59.418 1278 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.63 % Allowed : 10.95 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.25), residues: 1098 helix: -0.50 (0.21), residues: 654 sheet: 0.70 (0.56), residues: 82 loop : -1.65 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 396 TYR 0.012 0.002 TYR A 586 PHE 0.014 0.002 PHE A 499 TRP 0.011 0.002 TRP C 447 HIS 0.009 0.002 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8944) covalent geometry : angle 0.61881 (12134) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.87633 ( 4) hydrogen bonds : bond 0.05592 ( 358) hydrogen bonds : angle 4.01926 ( 1044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.354 Fit side-chains REVERT: A 136 LYS cc_start: 0.8883 (tptm) cc_final: 0.8560 (tptp) REVERT: A 491 MET cc_start: 0.8356 (tpp) cc_final: 0.8035 (tpt) REVERT: A 492 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: A 599 GLU cc_start: 0.7652 (tt0) cc_final: 0.5859 (pm20) REVERT: A 627 GLU cc_start: 0.8186 (mp0) cc_final: 0.7523 (mp0) REVERT: A 650 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.6102 (mtt90) REVERT: C 136 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8485 (tptp) REVERT: C 137 GLN cc_start: 0.7687 (mp10) cc_final: 0.7418 (mm-40) REVERT: C 403 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.7159 (p90) REVERT: C 491 MET cc_start: 0.8501 (tpp) cc_final: 0.8177 (tpt) REVERT: C 599 GLU cc_start: 0.7633 (tt0) cc_final: 0.5857 (pm20) REVERT: C 626 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7486 (pm20) REVERT: C 627 GLU cc_start: 0.8295 (mp0) cc_final: 0.7369 (mp0) REVERT: C 650 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.6105 (mtt90) outliers start: 25 outliers final: 16 residues processed: 106 average time/residue: 0.7125 time to fit residues: 79.8144 Evaluate side-chains 106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.132333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.100397 restraints weight = 9662.276| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.67 r_work: 0.2854 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8946 Z= 0.130 Angle : 0.542 8.060 12138 Z= 0.280 Chirality : 0.044 0.155 1442 Planarity : 0.005 0.075 1478 Dihedral : 7.110 62.053 1278 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.32 % Allowed : 11.37 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.26), residues: 1098 helix: -0.27 (0.21), residues: 652 sheet: 0.74 (0.56), residues: 82 loop : -1.54 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 402 TYR 0.010 0.001 TYR A 586 PHE 0.012 0.001 PHE A 499 TRP 0.010 0.001 TRP A 447 HIS 0.009 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8944) covalent geometry : angle 0.54154 (12134) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.63999 ( 4) hydrogen bonds : bond 0.04453 ( 358) hydrogen bonds : angle 3.90950 ( 1044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.368 Fit side-chains REVERT: A 136 LYS cc_start: 0.8852 (tptm) cc_final: 0.8533 (tptp) REVERT: A 491 MET cc_start: 0.8317 (tpp) cc_final: 0.7995 (tpt) REVERT: A 492 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: A 599 GLU cc_start: 0.7532 (tt0) cc_final: 0.5708 (pm20) REVERT: A 626 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7470 (pm20) REVERT: A 627 GLU cc_start: 0.8173 (mp0) cc_final: 0.7234 (mp0) REVERT: A 650 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.6097 (mtt90) REVERT: C 136 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8465 (tptp) REVERT: C 137 GLN cc_start: 0.7658 (mp10) cc_final: 0.7406 (mm-40) REVERT: C 402 ARG cc_start: 0.7698 (ttt-90) cc_final: 0.7381 (tpp80) REVERT: C 403 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.7045 (p90) REVERT: C 489 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7723 (mp) REVERT: C 491 MET cc_start: 0.8461 (tpp) cc_final: 0.8133 (tpt) REVERT: C 599 GLU cc_start: 0.7520 (tt0) cc_final: 0.5705 (pm20) REVERT: C 626 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7480 (pm20) REVERT: C 627 GLU cc_start: 0.8291 (mp0) cc_final: 0.7378 (mp0) REVERT: C 650 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.6104 (mtt90) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 0.7177 time to fit residues: 78.9422 Evaluate side-chains 110 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.133411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.101563 restraints weight = 9602.083| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.66 r_work: 0.2872 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8946 Z= 0.117 Angle : 0.523 7.375 12138 Z= 0.270 Chirality : 0.043 0.150 1442 Planarity : 0.004 0.076 1478 Dihedral : 6.936 62.925 1278 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.32 % Allowed : 11.58 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.26), residues: 1098 helix: -0.08 (0.21), residues: 650 sheet: 0.20 (0.46), residues: 110 loop : -1.52 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 431 TYR 0.010 0.001 TYR A 586 PHE 0.012 0.001 PHE C 499 TRP 0.010 0.001 TRP A 447 HIS 0.005 0.001 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8944) covalent geometry : angle 0.52285 (12134) SS BOND : bond 0.00053 ( 2) SS BOND : angle 0.61551 ( 4) hydrogen bonds : bond 0.04145 ( 358) hydrogen bonds : angle 3.84878 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2939.07 seconds wall clock time: 50 minutes 58.48 seconds (3058.48 seconds total)